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<li class="navelem"><a class="el" href="dir_2312589fb962dec58b1579fafe6a300a.html">cudamapper</a></li><li class="navelem"><a class="el" href="dir_46ada5e69ffe047ce1b425fcb02bc946.html">include</a></li><li class="navelem"><a class="el" href="dir_00faf102fbd78ece25aa2d8f2597f59b.html">claragenomics</a></li><li class="navelem"><a class="el" href="dir_5d9177f36fbce0c085b11d352d248d8a.html">cudamapper</a></li>  </ul>
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<div class="title">sketch_element.hpp</div>  </div>
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<div class="fragment"><div class="line"><a name="l00001"></a><span class="lineno">    1</span>&#160;<span class="comment">/*</span></div>
<div class="line"><a name="l00002"></a><span class="lineno">    2</span>&#160;<span class="comment">* Copyright (c) 2019, NVIDIA CORPORATION.  All rights reserved.</span></div>
<div class="line"><a name="l00003"></a><span class="lineno">    3</span>&#160;<span class="comment">*</span></div>
<div class="line"><a name="l00004"></a><span class="lineno">    4</span>&#160;<span class="comment">* NVIDIA CORPORATION and its licensors retain all intellectual property</span></div>
<div class="line"><a name="l00005"></a><span class="lineno">    5</span>&#160;<span class="comment">* and proprietary rights in and to this software, related documentation</span></div>
<div class="line"><a name="l00006"></a><span class="lineno">    6</span>&#160;<span class="comment">* and any modifications thereto.  Any use, reproduction, disclosure or</span></div>
<div class="line"><a name="l00007"></a><span class="lineno">    7</span>&#160;<span class="comment">* distribution of this software and related documentation without an express</span></div>
<div class="line"><a name="l00008"></a><span class="lineno">    8</span>&#160;<span class="comment">* license agreement from NVIDIA CORPORATION is strictly prohibited.</span></div>
<div class="line"><a name="l00009"></a><span class="lineno">    9</span>&#160;<span class="comment">*/</span></div>
<div class="line"><a name="l00010"></a><span class="lineno">   10</span>&#160; </div>
<div class="line"><a name="l00011"></a><span class="lineno">   11</span>&#160;<span class="preprocessor">#pragma once</span></div>
<div class="line"><a name="l00012"></a><span class="lineno">   12</span>&#160; </div>
<div class="line"><a name="l00013"></a><span class="lineno">   13</span>&#160;<span class="preprocessor">#include &lt;cstdint&gt;</span></div>
<div class="line"><a name="l00014"></a><span class="lineno">   14</span>&#160;<span class="preprocessor">#include &lt;memory&gt;</span></div>
<div class="line"><a name="l00015"></a><span class="lineno">   15</span>&#160;<span class="preprocessor">#include &lt;claragenomics/cudamapper/types.hpp&gt;</span></div>
<div class="line"><a name="l00016"></a><span class="lineno">   16</span>&#160; </div>
<div class="line"><a name="l00017"></a><span class="lineno">   17</span>&#160;<span class="keyword">namespace </span>claragenomics</div>
<div class="line"><a name="l00018"></a><span class="lineno">   18</span>&#160;{</div>
<div class="line"><a name="l00019"></a><span class="lineno">   19</span>&#160; </div>
<div class="line"><a name="l00020"></a><span class="lineno">   20</span>&#160;<span class="keyword">namespace </span>cudamapper</div>
<div class="line"><a name="l00021"></a><span class="lineno">   21</span>&#160;{</div>
<div class="line"><a name="l00024"></a><span class="lineno">   24</span>&#160; </div>
<div class="line"><a name="l00026"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html">   26</a></span>&#160;<span class="keyword">class </span><a class="code" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html">SketchElement</a></div>
<div class="line"><a name="l00027"></a><span class="lineno">   27</span>&#160;{</div>
<div class="line"><a name="l00028"></a><span class="lineno">   28</span>&#160;<span class="keyword">public</span>:</div>
<div class="line"><a name="l00030"></a><span class="lineno"><a class="line" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">   30</a></span>&#160;    <span class="keyword">enum class</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">DirectionOfRepresentation</a></div>
<div class="line"><a name="l00031"></a><span class="lineno">   31</span>&#160;    {</div>
<div class="line"><a name="l00032"></a><span class="lineno">   32</span>&#160;        FORWARD,</div>
<div class="line"><a name="l00033"></a><span class="lineno">   33</span>&#160;        REVERSE</div>
<div class="line"><a name="l00034"></a><span class="lineno">   34</span>&#160;    };</div>
<div class="line"><a name="l00035"></a><span class="lineno">   35</span>&#160; </div>
<div class="line"><a name="l00037"></a><span class="lineno">   37</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#ac62560de124742cb23bc1def0a0b2069">~SketchElement</a>() = <span class="keywordflow">default</span>;</div>
<div class="line"><a name="l00038"></a><span class="lineno">   38</span>&#160; </div>
<div class="line"><a name="l00041"></a><span class="lineno">   41</span>&#160;    <span class="keyword">virtual</span> representation_t <a class="code" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#abb3c8927594ba5f077c4443c229e0730">representation</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00042"></a><span class="lineno">   42</span>&#160; </div>
<div class="line"><a name="l00045"></a><span class="lineno">   45</span>&#160;    <span class="keyword">virtual</span> position_in_read_t <a class="code" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a0ddea36eed82ea3a9d1fa7ace61051bc">position_in_read</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00046"></a><span class="lineno">   46</span>&#160; </div>
<div class="line"><a name="l00049"></a><span class="lineno">   49</span>&#160;    <span class="keyword">virtual</span> <a class="code" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">DirectionOfRepresentation</a> <a class="code" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af4b53bc09f5816c3b81fef1c1abf3fc6">direction</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00050"></a><span class="lineno">   50</span>&#160; </div>
<div class="line"><a name="l00053"></a><span class="lineno">   53</span>&#160;    <span class="keyword">virtual</span> read_id_t <a class="code" href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af5f2e8fc8df725b336833930baf3cd39">read_id</a>() <span class="keyword">const</span> = 0;</div>
<div class="line"><a name="l00054"></a><span class="lineno">   54</span>&#160;};</div>
<div class="line"><a name="l00055"></a><span class="lineno">   55</span>&#160; </div>
<div class="line"><a name="l00057"></a><span class="lineno">   57</span>&#160; </div>
<div class="line"><a name="l00058"></a><span class="lineno">   58</span>&#160;} <span class="comment">// namespace cudamapper</span></div>
<div class="line"><a name="l00059"></a><span class="lineno">   59</span>&#160; </div>
<div class="line"><a name="l00060"></a><span class="lineno">   60</span>&#160;} <span class="comment">// namespace claragenomics</span></div>
</div><!-- fragment --></div><!-- contents -->
<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1SketchElement_html_af5f2e8fc8df725b336833930baf3cd39"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af5f2e8fc8df725b336833930baf3cd39">claragenomics::cudamapper::SketchElement::read_id</a></div><div class="ttdeci">virtual read_id_t read_id() const =0</div><div class="ttdoc">returns read ID</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1SketchElement_html_ac62560de124742cb23bc1def0a0b2069"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#ac62560de124742cb23bc1def0a0b2069">claragenomics::cudamapper::SketchElement::~SketchElement</a></div><div class="ttdeci">virtual ~SketchElement()=default</div><div class="ttdoc">Virtual destructor for SketchElement.</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1SketchElement_html_af4b53bc09f5816c3b81fef1c1abf3fc6"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#af4b53bc09f5816c3b81fef1c1abf3fc6">claragenomics::cudamapper::SketchElement::direction</a></div><div class="ttdeci">virtual DirectionOfRepresentation direction() const =0</div><div class="ttdoc">returns representation's direction</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1SketchElement_html_abb3c8927594ba5f077c4443c229e0730"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#abb3c8927594ba5f077c4443c229e0730">claragenomics::cudamapper::SketchElement::representation</a></div><div class="ttdeci">virtual representation_t representation() const =0</div><div class="ttdoc">returns integer representation of a kmer</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1SketchElement_html"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1SketchElement.html">claragenomics::cudamapper::SketchElement</a></div><div class="ttdoc">SketchElement - Contains integer representation, position, direction and read id of a kmer.</div><div class="ttdef"><b>Definition:</b> sketch_element.hpp:26</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1SketchElement_html_a83beb5c091c4b0bfec99c04b6bc8777a"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a83beb5c091c4b0bfec99c04b6bc8777a">claragenomics::cudamapper::SketchElement::DirectionOfRepresentation</a></div><div class="ttdeci">DirectionOfRepresentation</div><div class="ttdoc">Is this a representation of forward or reverse compliment.</div><div class="ttdef"><b>Definition:</b> sketch_element.hpp:30</div></div>
<div class="ttc" id="aclassclaragenomics_1_1cudamapper_1_1SketchElement_html_a0ddea36eed82ea3a9d1fa7ace61051bc"><div class="ttname"><a href="classclaragenomics_1_1cudamapper_1_1SketchElement.html#a0ddea36eed82ea3a9d1fa7ace61051bc">claragenomics::cudamapper::SketchElement::position_in_read</a></div><div class="ttdeci">virtual position_in_read_t position_in_read() const =0</div><div class="ttdoc">returns position of the sketch in the read</div></div>
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